For maintainability reasons, I want to database drive my javascript, in that I only want to send the javascript which is needed based on the users options.
So, is it faster/less resource heavy to have links in the database pointing to javascript files, then using response.writefile to embed those files into the clientside page, or is it faster/less resource heavy to stick the javascript script straight into the database, and response.write it onto the screen as and when needed?
Usually yes.
External Javascript files can be cached by the browser, and will be loaded only once. Javascript code injected into the HTML page needs to be loaded every time, which increases bandwidth and loading times.
Also, having JavaScript code in a static file (instead of a dynamic one that fetches the code from the database on every request) is bound to be the fastest and least resource-intensive solution.